[Biopython] Translation of partial codons

[Iddo Friedberg]

I tend to agree with Peter rather than with myself :)  If the current
behavior is a bug, we should squash it.

On Thu, Mar 21, 2013 at 1:19 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Thu, Mar 21, 2013 at 5:10 PM, Iddo Friedberg <idoerg at gmail.com> wrote:
> > Suggstions so far:
> > 1. Raise an exception. This may cause  code running on existing data to
> > change behavior. I.e. it ran before well on bad length sequences, but as
> of
> > the new code installtion, things will break.
>
> Yes, but in most cases this will be a good thing. The minority of people
> knowingly dealing with partial sequences can make this explicit by first
> ensuring their sequence is a multiple of three in length (by padding or
> cropping as most appropriate to their use case).
>
> > 2. Add a default length_check=True to the translate method. Again, this
> may
> > cause exiting code to behave differently wiht the same data once user
> > upgrades. Unless the user explicitly changes the call to
> > myseq.translate(length_check=False)
>
> A sensible approach to making likely errors explicit, with an easy
> work-around
> for the old implicit truncation. The downside is yet another argument to
> the
> translate functions/methods, which are already pretty complicated. I
> prefer (1).
>
> > 3. My suggestion: use length_check=False as default. Code behaves the
> same
> > as before, so no data-induced breakages. If the user wants to check
> length,
> > the explicitly pass a True value. So we give the option of checking
> length,
> > and retaining code-behavior legacy.
> >
> > length_check, being an argument, does not need to be passed explicitly.
>
> I don't like this, even though it is backwards compatible for the corner
> case. I think the old behaviour is a bug.
>
> Regards,
>
> Peter
>



-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html
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